| Variant ID: vg1227343327 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 27343327 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.01, others allele: 0.00, population size: 295. )
GGGCCATGCAAGCTGTTCTGGTGCAATGCTCTGAACAAAAGGGGTTAGAAATTAAAGAAAGACCAATGCGGATAGTGTAAATGAAGATGGTGTTGAAATG[G/T]
GAAGTGTTGCACAAAAGTGGTGAAGAAGAAAAAATGTTACATTCTCTGCAGCTTGTCGAGCTTCCCAATGTTAGGTGAAATGATGCCCCCAAGCTGCATG
CATGCAGCTTGGGGGCATCATTTCACCTAACATTGGGAAGCTCGACAAGCTGCAGAGAATGTAACATTTTTTCTTCTTCACCACTTTTGTGCAACACTTC[C/A]
CATTTCAACACCATCTTCATTTACACTATCCGCATTGGTCTTTCTTTAATTTCTAACCCCTTTTGTTCAGAGCATTGCACCAGAACAGCTTGCATGGCCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.20% | 24.50% | 0.19% | 0.11% | NA |
| All Indica | 2759 | 58.70% | 40.80% | 0.33% | 0.18% | NA |
| All Japonica | 1512 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 81.70% | 18.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 76.80% | 22.80% | 0.22% | 0.22% | NA |
| Indica III | 913 | 38.40% | 61.00% | 0.22% | 0.33% | NA |
| Indica Intermediate | 786 | 54.20% | 45.20% | 0.51% | 0.13% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 14.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1227343327 | G -> DEL | N | N | silent_mutation | Average:60.584; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |
| vg1227343327 | G -> T | LOC_Os12g44100.1 | downstream_gene_variant ; 2795.0bp to feature; MODIFIER | silent_mutation | Average:60.584; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |
| vg1227343327 | G -> T | LOC_Os12g44090.1 | intron_variant ; MODIFIER | silent_mutation | Average:60.584; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |